cnodata | A cnodata from CellNoptR |
cnolist | A cnolist from CellNoptR |
cnolistCNORodeExample | A cnolist from CellNoptR |
CNORode | Logic based ODE extension for CellNOptR |
createLBodeContPars | Create a list with ODE parameter information needed to perform parameter estimation |
crossvalidateODE | k-fold crossvalidation for ODE models. |
defaultParametersGA | Create default options to perform parameter estimation with a genetic algorithm. |
defaultParametersSSm | Create default options to perform parameter estimation with scatter search meta-heuristic. |
getLBodeContObjFunction | Returns the objective function to perform parameter estimation. |
getLBodeDataSim | Simulate value signals a CNO list With Logic-Based ODEs. |
getLBodeMINLPObjFunction | Get the objective function to evaluate the fitness of a given model structure and set of parameters. |
getLBodeModelSim | Simulate the logic-based ODE model |
getLBodeSimFunction | Get a function to simulate a logic based ODE model. |
getStates | Find which species in the model are states. |
incidence2Adjacency | Convert an incidence matrix into an adjacency matrix. |
indices | Indices that relate cnolist to model |
minlpLBodeSSm | Search for the best combination of continuous parameters and logic gates. |
model | A model from CellNoptR |
parEstimationLBode | Perform parameter estimation using a genetic algorithm (package genalg) or ssm (if package essm available). |
parEstimationLBodeGA | Perform parameter estimation using a genetic algorithm (package genalg). |
parEstimationLBodeSSm | Perform parameter estimation using essR. |
pknmodel | A pknmodel from CellNoptR |
plotLBodeFitness | Plot data against simulated values. |
plotLBodeModelSim | Simulate the model and plot the obtained with the different experimental conditions. |
runCNORode | runCNORode |
simdata2cnolist | converts output of getLBodeModelSim to cnolist |
simulate | Simulate value signals a CNO list With Logic-Based ODEs. |